My favorites are:
1) Freaky Flyers (Gamecube), for the refreshing hardcore difficulty, hilarious cut-scenes, and objective-based gameplay and side missions- it dared to be different.
2) Mariokart Double Dash (Gamecube), for the hold item mechanics, introduction of customizable karts and overabundance of unlockables.
3) Mariokart DS (NDS), for the boss battles and single-player missions that made this one a longer experience for me than most Mariokarts, and the inclusion of bots and teams for battle mode and download-play options for up to 8 people.

Beyond Good and Evil 2 better be happening! In the meanwhile though, here's a fun little Let's Play of the original. Think you'll like the game if you like Zelda!LeT's PlAy BEYOND GOOD AND EVIL < Link to LP